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Plants use light as a resource and signal. Photons within the 400-700 nm waveband are considered photosynthetically active. Far-red photons (FR, 700-800 nm) are used by plants to detect nearby vegetation and elicit the shade avoidance syndrome. In addition, FR photons have also been shown to contribute to photosynthesis, but knowledge about these dual effects remains scarce. Here, we study shoot-architectural and photosynthetic responses to supplemental FR light during the photoperiod in several rice varieties. We observed that FR enrichment only mildly affected the rice transcriptome and shoot architecture as compared to established model species, whereas leaf formation, tillering and biomass accumulation were clearly promoted. Consistent with this growth promotion, we found that CO 2 -fixation in supplemental FR was strongly enhanced, especially in plants acclimated to FR-enriched conditions as compared to control conditions. This growth promotion dominates the effects of FR photons on shoot development and architecture. When substituting FR enrichment with an end-of-day FR pulse, this prevented photosynthesis-promoting effects and elicited shade avoidance responses. We conclude that FR photons can have a dual role, where effects depend on the environmental context: in addition to being an environmental signal, they are also a potent source of harvestable energy., (© 2024 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Plant leaves contain multiple cell types which achieve distinct characteristics whilst still coordinating development within the leaf. The bundle sheath possesses larger individual cells and lower chloroplast content than the adjacent mesophyll, but how this morphology is achieved remains unknown. To identify regulatory mechanisms determining bundle sheath cell morphology we tested the effects of perturbing environmental (light) and endogenous signals (hormones) during leaf development of Oryza sativa (rice). Total chloroplast area in bundle sheath cells was found to increase with cell size as in the mesophyll but did not maintain a 'set-point' relationship, with the longest bundle sheath cells demonstrating the lowest chloroplast content. Application of exogenous cytokinin and gibberellin significantly altered the relationship between cell size and chloroplast biosynthesis in the bundle sheath, increasing chloroplast content of the longest cells. Delayed exposure to light reduced the mean length of bundle sheath cells but increased corresponding leaf length, whereas premature light reduced final leaf length but did not affect bundle sheath cells. This suggests that the plant hormones cytokinin and gibberellin are regulators of the bundle sheath cell-chloroplast relationship and that final bundle sheath length may potentially be affected by light-mediated control of exit from the cell cycle., (© 2024 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model photosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosynthetic parameters using concurrent gas exchange and chlorophyll fluorescence measurements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, K m , that is, Michaelis constant for CO 2 by Rubisco, prefixed. Additionally, we show that including detailed low CO 2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement protocols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided., (© 2021 John Wiley & Sons Ltd.)

Responses of rice seedlings to UV-B radiation (UV-B) were investigated, aiming to establish rice as a model plant for UV-B signalling studies. The growth of japonica rice coleoptiles, grown under red light, was inhibited by brief irradiation with UV-B, but not with blue light. The effective UV-B fluences (10 -1 -10 3 μmol m -2 ) were much lower than those reported in Arabidopsis. The response was much less in indica rice cultivars and its extent varied among Oryza species. We next identified UV-B-specific anthocyanin accumulation in the first leaf of purple rice and used this visible phenotype to isolate mutants. Some isolated mutants were further characterized, and one was found to have a defect in the growth response. Using microarrays, we identified a number of genes that are regulated by low-fluence-rate UV-B in japonica coleoptiles. Some up-regulated genes were analysed by real-time PCR for UV-B specificity and the difference between japonica and indica. More than 70% of UV-B-regulated rice genes had no homologs in UV-B-regulated Arabidopsis genes. Many UV-B-regulated rice genes are related to plant hormones and especially to jasmonate biosynthetic and responsive genes in apparent agreement with the growth response. Possible involvement of two rice homologs of UVR8, a UV-B photoreceptor, is discussed., (© 2020 John Wiley & Sons Ltd.)

Long-term fluctuating light (FL) conditions are very common in natural environments. The physiological and biochemical mechanisms for acclimation to FL differ between species. However, most of the current conclusions regarding acclimation to FL were made based on studies in algae or Arabidopsis thaliana. It is still unclear how rice (Oryza sativa L.) integrate multiple physiological changes to acclimate to long-term FL. In this study, we found that rice growth was repressed under long-term FL. By systematically measuring phenotypes and physiological parameters, we revealed that: (a) under short-term FL, photosystem I (PSI) was inhibited, while after 1-7 days of long-term FL, both PSI and PSII were inhibited. Higher acceptor-side limitation in electron transport and higher overall nonphotochemical quenching (NPQ) explained the lower efficiencies of PSI and PSII, respectively. (b) An increase in pH differences across the thylakoid membrane and a decrease in thylakoid proton conductivity revealed a reduction of ATP synthase activity. (c) Using electron microscopy, we showed a decrease in membrane stacking and stomatal opening after 7 days of FL treatment. Taken together, our results show that electron flow, ATP synthase activity and NPQ regulation are the major processes determining the growth performance of rice under long-term FL conditions., (© 2020 John Wiley & Sons Ltd.)

A close correlation between stomatal conductance and the steady-state photosynthetic rate has been observed for diverse plant species under various environmental conditions. However, it remains unclear whether stomatal conductance is a major limiting factor for the photosynthetic rate under naturally fluctuating light conditions. We analysed a SLAC1 knockout rice line to examine the role of stomatal conductance in photosynthetic responses to fluctuating light. SLAC1 encodes a stomatal anion channel that regulates stomatal closure. Long exposures to weak light before treatments with strong light increased the photosynthetic induction time required for plants to reach a steady-state photosynthetic rate and also induced stomatal limitation of photosynthesis by restricting the diffusion of CO 2 into leaves. The slac1 mutant exhibited a significantly higher rate of stomatal opening after an increase in irradiance than wild-type plants, leading to a higher rate of photosynthetic induction. Under natural conditions, in which irradiance levels are highly variable, the stomata of the slac1 mutant remained open to ensure efficient photosynthetic reaction. These observations reveal that stomatal conductance is important for regulating photosynthesis in rice plants in the natural environment with fluctuating light., (© 2020 John Wiley & Sons Ltd.)

To further our understanding of how sustained changes in temperature affect the carbon economy of rice (Oryza sativa), hydroponically grown plants of the IR64 cultivar were developed at 30°C/25°C (day/night) before being shifted to 25/20°C or 40/35°C. Leaf messenger RNA and protein abundance, sugar and starch concentrations, and gas-exchange and elongation rates were measured on preexisting leaves (PE) already developed at 30/25°C or leaves newly developed (ND) subsequent to temperature transfer. Following a shift in growth temperature, there was a transient adjustment in metabolic gene transcript abundance of PE leaves before homoeostasis was reached within 24 hr, aligning with R dark (leaf dark respiratory CO 2 release) and A n (net CO 2 assimilation) changes. With longer exposure, the central respiratory protein cytochrome c oxidase (COX) declined in abundance at 40/35°C. In contrast to R dark , A n was maintained across the three growth temperatures in ND leaves. Soluble sugars did not differ significantly with growth temperature, and growth was fastest with extended exposure at 40/35°C. The results highlight that acclimation of photosynthesis and respiration is asynchronous in rice, with heat-acclimated plants exhibiting a striking ability to maintain net carbon gain and growth when exposed to heat-wave temperatures, even while reducing investment in energy-conserving respiratory pathways., (© 2019 John Wiley & Sons Ltd.)

We studied physiological mechanisms of photoavoidance and photoprotection of a dwarf rice mutant with erect leaves, d1, in which the RGA1 gene, which encodes the Gα subunit of the heterotrimeric G protein, is non-functional. Leaves of d1 exhibit lower leaf temperature and higher photochemical reflectance index relative to wild type (WT), indicative of increased photoavoidance and more efficient light harvesting. RNA sequencing analysis of flag leaves revealed that messenger RNA levels of genes encoding heat shock proteins, enzymes associated with chlorophyll breakdown, and ROS scavengers were down-regulated in d1. By contrast, genes encoding proteins associated with light harvesting, Photosystem II, cyclic electron transport, Photosystem I, and chlorophyll biosynthesis were up-regulated in d1. Consistent with these observations, when WT and d1 plants were experimentally subjected to the same light intensity, d1 plants exhibited a greater capacity to dissipate excess irradiance (increased nonphotochemical quenching) relative to WT. The increased capacity in d1 for both photoavoidance and photoprotection reduced sustained photoinhibitory damage, as revealed by a higher F v /F m . We therefore propose RGA1 as a regulator of photoavoidance and photoprotection mechanisms in rice and highlight the prospect of exploiting modulation of heterotrimeric G protein signalling to increase these characteristics and improve the yield of cereals in the event of abiotic stress., (© 2017 John Wiley & Sons Ltd.)

Photosynthesis in C3 plants is significantly limited by mesophyll conductance (gm ), which can vary with leaf anatomical traits and nitrogen (N) supplements. Several studies have investigated the response of gm to N supplements; however, none examined the implications of N supplements on the response of gm to rapid environmental changes. Here we investigated the effect of N supplement on gm and the response of gm to change of CO2 , temperature and irradiance in rice. High N supplement (HN) increased mesophyll cell wall surface area and chloroplast surface area exposed to intercellular airspace per leaf area, and reduced cell wall thickness. These changes resulted in increased gm . The gm of leaves with HN was more sensitive to changes in CO2 concentration, temperature and irradiance. The difference in leaf structural features between low N supplement and HN indicates that a rapid change in gm is related to the regulation of diffusion through biological membranes rather than leaf structural features. These results will contribute to an understanding of the determinants of gm response to rapid changes in environmental factors., (© 2015 John Wiley & Sons Ltd.)

In the facultative long-day (LD) plant Arabidopsis thaliana, FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) is activated by blue light and promotes flowering through the transcriptional and post-translational regulation of CONSTANS under inductive LD conditions. By contrast, the facultative short day (SD) plant rice (Oryza sativa) flowers early under inductive SD and late under non-inductive LD conditions; the regulatory function of OsFKF1 remains elusive. Here we show that osfkf1 mutants flower late under SD, LD and natural LD conditions. Transcriptional analysis revealed that OsFKF1 up-regulates the expression of the floral activator Ehd2 and down-regulates the expression of the floral repressor Ghd7; these regulators up- and down-regulate Ehd1 expression, respectively. Moreover, OsFKF1 can up-regulate Ehd1 expression under blue light treatment, without affecting the expression of Ehd2 and Ghd7. In contrast to the LD-specific floral activator Arabidopsis FKF1, OsFKF1 likely acts as an autonomous floral activator because it promotes flowering independent of photoperiod, probably via its distinct roles in controlling the expression of rice-specific genes including Ehd2, Ghd7 and Ehd1. Like Arabidopsis FKF1, which interacts with GI and CDF1, OsFKF1 also interacts with OsGI and OsCDF1 (also termed OsDOF12). Thus, we have identified similar and distinct roles of FKF1 in Arabidopsis and rice., (© 2015 John Wiley & Sons Ltd.)

The physiological role of peroxisomal ascorbate peroxidases (pAPX) is unknown; therefore, we utilized pAPX4 knockdown rice and catalase (CAT) inhibition to assess its role in CAT compensation under high photorespiration. pAPX4 knockdown induced co-suppression in the expression of pAPX3. The rice mutants exhibited metabolic changes such as lower CAT and glycolate oxidase (GO) activities and reduced glyoxylate content; however, APX activity was not altered. CAT inhibition triggered different changes in the expression of CAT, APX and glutathione peroxidase (GPX) isoforms between non-transformed (NT) and silenced plants. These responses were associated with alterations in APX, GPX and GO activities, suggesting redox homeostasis differences. The glutathione oxidation-reduction states were modulated differently in mutants, and the ascorbate redox state was greatly affected in both genotypes. The pAPX suffered less oxidative stress and photosystem II (PSII) damage and displayed higher photosynthesis than the NT plants. The improved acclimation exhibited by the pAPX plants was indicated by lower H2 O2 accumulation, which was associated with lower GO activity and glyoxylate content. The suppression of both pAPXs and/or its downstream metabolic and molecular effects may trigger favourable antioxidant and compensatory mechanisms to cope with CAT deficiency. This physiological acclimation may involve signalling by peroxisomal H2 O2 , which minimized the photorespiration., (© 2014 John Wiley & Sons Ltd.)

Phytochromes are red- and far red light photoreceptors in higher plants. Rice (Oryza sativa L.) has three phytochromes (phyA, phyB and phyC), which play distinct as well as cooperative roles in light perception. To gain a better understanding of individual phytochrome functions in rice, expression patterns of three phytochrome genes were characterized using promoter-GUS fusion constructs. The phytochrome genes PHYA and PHYB showed distinct patterns of tissue- and developmental stage-specific expression in rice. The PHYA promoter-GUS was expressed in all leaf tissues in etiolated seedlings, while its expression was restricted to vascular bundles in expanded leaves of light-grown seedlings. These observations suggest that light represses the expression of the PHYA gene in all cells except vascular bundle cells in rice seedlings. Red light was effective, but far red light was ineffective in gene repression, and red light-induced repression was not observed in phyB mutants. These results indicate that phyB is involved in light-dependent and tissue-specific repression of the PHYA gene in rice., (© 2014 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

Some terrestrial wetland plants, such as rice, have super-hydrophobic leaf surfaces which retain a gas film when submerged. O2 movement through the diffusive boundary layer (DBL) of floodwater, gas film and stomata into leaf mesophyll was explored by means of a reaction-diffusion model that was solved in a three-dimensional leaf anatomy model. The anatomy and dark respiration of leaves of rice (Oryza sativa L.) were measured and used to compute O2 fluxes and partial pressure of O2 (pO2 ) in the DBL, gas film and leaf when submerged. The effects of floodwater pO2 , DBL thickness, cuticle permeability, presence of gas film and stomatal opening were explored. Under O2 -limiting conditions of the bulk water (pO2  < 10 kPa), the gas film significantly increases the O2 flux into submerged leaves regardless of whether stomata are fully or partly open. With a gas film, tissue pO2 substantially increases, even for the slightest stomatal opening, but not when stomata are completely closed. The effect of gas films increases with decreasing cuticle permeability. O2 flux and tissue pO2 decrease with increasing DBL thickness. The present modelling analysis provides a mechanistic understanding of how leaf gas films facilitate O2 entry into submerged plants., (© 2014 John Wiley & Sons Ltd.)

The bioactive form of jasmonate is the conjugate of the amino acid isoleucine (Ile) with jasmonic acid (JA), which is biosynthesized in a reaction catalysed by the GH3 enzyme JASMONATE RESISTANT 1 (JAR1). We examined the biochemical properties of OsJAR1 and its involvement in photomorphogenesis of rice (Oryza sativa). OsJAR1 has a similar substrate specificities as its orthologue in Arabidopsis. However, osjar1 loss-of-function mutants did not show as severe coleoptile phenotypes as the JA-deficient mutants coleoptile photomorphogenesis 2 (cpm2) and hebiba, which develop long coleoptiles in all light qualities we examined. Analysis of hormonal contents in the young seedling stage revealed that osjar1 mutants are still able to synthesize JA-Ile conjugate in response to blue light, suggesting that a redundantly active enzyme can conjugate JA and Ile in rice seedlings. A good candidate for this enzyme is OsJAR2, which was found to be able to catalyse the conjugation of JA with Ile as well as with some additional amino acids. In contrast, if plants in the vegetative stage were mechanically wounded, the content of JA-Ile was severely reduced in osjar1, demonstrating that OsJAR1 is the most important JA-Ile conjugating enzyme in the wounding response during the vegetative stage., (© 2013 John Wiley & Sons Ltd.)

Natural variation in heading-date genes enables rice, a short-day (SD) plant, to flower early under long-day (LD) conditions at high latitudes. Through analysis of heading-date quantitative trait loci (QTL) with F7 recombinant inbred lines from the cross of early heading 'H143' and late heading 'Milyang23 (M23)', we found a minor-effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/CKI in H143 and Koshihikari are non-functional. In F7:9 heterogeneous inbred family-near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD-dependent flowering repressor, down-regulating Ehd1 expression. In the world rice collection, two types of non-functional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions., (© 2013 John Wiley & Sons Ltd.)

Plants have evolved a remarkable capacity to track and respond to fluctuations of light quality and intensity that influence photomorphogenesis facilitated through several photoreceptors, which include a small family of phytochromes. Rice seedlings grown on germination paper in red light for 48 h having their shoot bottom exposed had suppressed photomorphogenesis and were deficient in chlorophyll. Seedlings grown under identical light regime having their shoot bottom covered were green and accumulated chlorophyll. Further, etiolated seedlings with their shoot bottom exposed, when grown in 4 min red/far-red cycles for 48 h, accumulated chlorophyll demonstrating the reversal of suppression of photomorphogenesis by far-red light. It implicates the involvement of phytochrome. Immunoblot analysis showed the persistence of photolabile phytochrome A protein for 48 h in seedlings grown in red light with their shoot bottom exposed, suggesting its involvement in suppression of photomorphogenesis. This was further corroborated in phyA seedlings that turned green when grown in red light having their shoot bottom exposed. Calmodulin (CaM) antagonist N-(6-aminohexyl)-5-chloro-1-napthalene sulphonamide or trifluoperazine substantially restored photomorphogenesis both in the wild type (WT) and phyA demonstrating the involvement of CaM-dependent kinases in the down-regulation of the greening process. Results demonstrate that red light-induced suppression of photomorphogenesis, perceived in the shoot bottom, is a red high irradiance response of PhyA., (© 2013 John Wiley & Sons Ltd.)

It has been found that coleoptiles of dark-grown rice (Oryza sativa L.) seedlings undergo regular circumnutation in circular orbits with periods of about 180 min. Both clockwise and counter-clockwise movements were observed, but individual coleoptiles continued to rotate only in one direction. Light-grown seedlings did not show circumnutation. In fact, dark-grown seedlings were found to cease circumnutating in response to a pulse of red light (R). This light-induced inhibition of circumnutation was demonstrated to involve both a FR-inducible very-low-fluence response, solely mediated by phytochrome A, and a FR-reversible low-fluence response, mediated by phytochrome B and/or C. The R-induced inhibition of circumnutation showed temporal agreement with the R-induced inhibition of coleoptile growth, suggesting that the former results from the latter. However, about 25% of growth activity remained after R treatment, indicating that circumnutation is more specifically regulated by phytochrome. The R-treated coleoptile showed gravitropism. Investigation of the growth differential for gravitropic curvature revealed that gravitropic responsiveness was rather enhanced by R. The results suggested that gravitropism is not a cause of circumnutation. It remained probable, however, that gravity perception is a part of the mechanism of circumnutation. It is speculated that the circumnutation investigated aids the seedling shoot in growing through the soil.